PEtab changelog

0.1 series

0.1.4

Library:

  • Fixes / updates in functions for computing llh and chi2

  • Allow and require output parameters defined in observable table to be defined in parameter table

  • Fix merge_preeq_and_sim_pars_condition which incorrectly assumed lists instead of dicts

  • Update parameter mapping to deal with species and compartments in condition table

  • Removed petab.migrations.sbml_observables_to_table

    For converting older PEtab files to observable table format, use one of the previous releases

  • Visualization:

    • Fix various issues with get_data_to_plot
    • Fixed various issues with expected presence of optional columns

0.1.3

File format:

  • Updated documentation
  • Observables table in YAML file now mandatory in schema (was implicitly mandatory before, as observable table was required already)

Library:

  • petablint:
    • Fix: allow specifying observables file via CLI (Closes #302)
    • Fix: nominalValue is optional unless estimated!=1 anywhere (Fixes #303)
    • Fix: handle undefined observables more gracefully (Closes #300) (#351)
  • Parameter mapping:
    • Fix / refactor parameter mapping (breaking change) (#344) (now performing parameter value and scale mapping together)
    • check optional measurement cols in mapping (#350)
  • allow calculating llhs (#349), chi2 values (#348) and residuals (#345)
  • Visualization
    • Basic Scatterplots & lot of bar plot fixes (#270)
    • Fix incorrect length of bool bool_preequ when subsetting with ind_meas (Closes #322)
  • make libcombine optional (#338)

0.1.2

Library:

  • Extensions and fixes for the visualization functions (#255, #262)
  • Allow to extract fixed|free and scaled|non-scaled parameters (#256, #268, #273)
  • Various fixes (esp. #264)
  • Add function to get observable ids (#269)
  • Improve documentation (esp. #289)
  • Set default column for simulation results to ‘simulation’
  • Add support for COMBINE archives (#271)
  • Fix sbml observables to table
  • Improve prior and dataframe tests (#285, #286, #297)
  • Add function to get parameter table with all default values (#288)
  • Move tests to github actions (#281)
  • Check for valid identifiers
  • Fix handling of empty values in dataframes
  • Allow to get numeric values in parameter mappings in scaled form (#308)

0.1.1

Library:

  • Fix parameter mapping: include output parameters not present in SBML model
  • Fix missing petab/petab_schema.yaml in source distribution
  • Let get_placeholders return an (ordered) list of placeholders
  • Deprecate petab.problem.from_folder and related functions (obsolete after introducing more flexible YAML files for grouping tables and models)

0.1.0

Data format:

  • Introduce observables table instead of SBML assignment rules for defining observation model (#244) (moves observableTransformation and noiseModel from the measurement table to the observables table)
  • Allow initial concentrations / sizes in condition table (#238)
  • Fixes and clarifications in the format documentation
  • Changes in prior columns of the parameter table (#222)
  • Introduced separate version number of file format, this release being version 1

Library:

  • Adaptations to new file formats
  • Various bugfixes and clean-up, especially in visualization and validator
  • Parameter mapping changed to include all model parameters and not only those differing from the ones defined inside the SBML model
  • Introduced constants for all field names and string options, replacing most string literals in the code (#228)
  • Added unit tests and additional format validation steps
  • Optional parallelization of parameter mapping (#205)
  • Extended documentation (in-source and example Jupyter notebooks)

0.0.2

Bugfix release

  • Fix petablint error
  • Fix minor issues in petab.visualize

0.0.1

Data format:

  • Update format and documentation with respect to data and parameter scales (#169)
  • Define YAML schema for grouping PEtab files, also allowing for more complex combinations of files (#183)

Library:

  • Refactor library. Reorganize petab.core functions.
  • Fix visualization w/o condition names #142
  • Extend validator
  • Removed deprecated functions petab.Problem.get_constant_parameters and petab.sbml.constant_species_to_parameters
  • Minor fixes and extensions

0.0 series

0.0.0a17

Data format: No changes

Library:

  • Extended visualization support
  • Add helper function and test case to deal with timepoint-specific parameters flatten_timepoint_specific_output_overrides (#128) (Closes #125)
  • Fix get_noise_distributions: so far we got ‘normal’ everywhere due to wrong grouping (#147)
  • Fix create_parameter_df: Exclude rule targets (#149)
  • Verify condition table column names occur as model parameters (Closes #150) (#151)
  • More informative error messages in case of wrongly set observable and noise parameters (Closes #118) (#155)
  • Update doc for copasi import and github installation (#158)
  • Extend validator to check if all required parameters are present in parameter table (Closes #43) (#159)
  • Setup documentation for RTD (#161)
  • Handle None in petab.core.split_parameter_replacement_list (Closes #121)
  • Fix(lint) correct handling of optional columns. Check before access.
  • Remove obsolete generate_experiment_id.py (Closes #111) #166

0.0.0a16 and earlier

See git history